109 Works

ModelMuse version 4.2

Richard B Winston
ModelMuse is a graphical user interface (GUI) for the U.S. Geological Survey (USGS) models MODFLOW 6, MODFLOW 2005, MODFLOW LGR, MODFLOW LGR2, MODFLOW NWT, MODFLOW CFP, MODFLOW OWHM, MODPATH, ZONEBUDGET, PHAST, SUTRA 2.2, SUTRA 3.0, MT3D USGS, and WellFootprint and the non USGS model MT3DMS. This software package provides a GUI for creating the flow and transport input file for PHAST and the input files for the other models. In ModelMuse, the spatial data for...

Software Release ModelMuse Version 4.1

Richard B Winston

Geophysical Bayesian Inference in Python

Foks, Nathan (Leon) L & Burke J Minsley

Rasterized Building Footprints

Foks, Nathan (Leon) L & Mehdi Heris

Runoff Modeling Services

Tara A. Gross, Jeremy K. Newson & Michael S. Kohn

libcomcat Software Release

Mike Hearne & Heather E Schovanec
libcomcat is a project designed to provide a Python equivalent to the ANSS ComCat search API. This includes a Python library that provides various classes and functions wrapping around the ComCat API, and a number of command line programs that use those functions.

Wild horse aerial double observer survey analysis R script

Stefan L. Ekernas
This R file estimates horse abundance by analyzing data from simultaneous double-observer aerial surveys. The code follows analytical procedures established by Dr. Bruce Lubow, the statistician contracted for many years by Bureau of Land Management (BLM). Field data collection techniques are described in the Standard Operating Procedures (SOPs), which is a separate document. Download the files "SDO_RMark_template.R" and "Example_data.csv" to the same directory. Open R and make this the working directory with File | Change...

DTSGUI

Marian Domanski & Frederick D Day-Lewis
This software release presents DTSGUI, a public-domain Python-based software package for editing, parsing, processing, statistical analysis, georeferencing, and visualization of FO-DTS data. Suggested citation: Domanski, M. and Day-Lewis, F.D., 2019, DTSGUI, U.S. Geological Survey software release, https://doi.org/10.5066/P91Z7ZAZ.

popcluster: Developing Hierarchical Population Monitoring Frameworks for mobile species with high site fidelity

Michael S. O'Donnell, David R. Edmunds, Cameron L. Aldridge, Julie A. Heinrichs, Peter S. Coates, Brian G. Prochazka & Steve E. Hanser
The software "popcluster" constructs hierarchically nested groupings of similar habitats associated with field surveys while considering biological structure/connectedness (movements between habitats). This approach can support mobile species with high site fidelity where monitoring during surveys occurs on birthing grounds, breeding grounds, or stopovers/seasonal habitat for migratory species. Each nested level of the resulting hierarchical monitoring framework will represent an increasing number of similarly clustered survey observation sites allowing for comparisons of population changes across spatial...

eDNAoccupancy

Robert M. Dorazio & Richard A. Erickson
This repository contains the source code and package for the eDNAoccupancy package. This readme file contains the installation instructions for the package. The purpose of the R package is to fit three-level occupancy models. Although designed with eDNA-based observations, the package can be used for any occupancy situation with sampling and sub-sampling.

Quality control tools for seismic catalogs (qc_report and qc_multi)

Nicholas Ambruz
Generate plots and statistics for single earthquake catalogs and for catalog to catalog comparisons.

R code for fitting and simulation study for zero-augmented beta model with errors

Kathryn M Irvine, Wilson J. Wright, Jeffrey M. Warren & Jenny K. Barnett
Code for implementing the Zero-Augmented Beta Model with Errors (ZABE) , simulation study code, and code for assessing trade-offs in study design via simulations.

Code release for bat data analyses in Modelling misclassification in multi-species acoustic data when estimating occupancy and relative activity

Wilson J Wright, Kathryn M Irvine, Emily S. Almberg & Andrea R. Litt

Software Supplement to accompany "Estimating Species-Environment Relationships with Non-ignorable Sampling Designs"

Kathryn M Irvine, Thomas J. Rodhouse, Wilson J. Wright & Anthony R. Olsen
R code to fit models with and without sample weights and simulation code

Online supporting information for "Statistical power of dynamic occupancy models to identify temporal change: informing the North American Bat Monitoring Program"

Katharine M. Banner, Kathryn M Irvine, Thomas J. Rodhouse, Deahn Donner & Andrea R. Litt

Online supporting information for "Improving geographically extensive acoustic survey designs for modeling species occurrence with imperfect detection and misidentification"

Rogelio M. Rodriguez, Wilson J. Wright, Katharine M. Banner, Andrea R. Litt, Kathryn M Irvine & Thomas J. Rodhouse
R package developed to support study design for acoustic bat surveys with imperfect detection misidentification

Supplement S1: Code Release for fitting OZAB and OZABE to Empirical Datasets in "Cohesive Framework for Modeling Plant Cover Class Data"

Kathryn M Irvine, Wilson J. Wright, Thomas J. Rodhouse & Erin K. Shanahan

Sediment Source Assessment Tool (Sed_SAT)

Lillian Gorman Sanisaca, Allen Gellis & David Lorenz
A sound understanding of sources contributing to instream sediment flux in a watershed is important when developing total maximum daily load (TMDL) management strategies designed to reduce suspended sediment in streams. Sediment fingerprinting and sediment budget approaches are two techniques, that when used jointly, can qualify and quantify the major sources of sediment in a given watershed. The sediment fingerprinting approach uses trace element concentrations from samples in known potential source areas to determine a...

Point-Source Load Estimation Tool (PSLoadEsT)

Lillian Gorman Sanisaca, Kenneth D. Skinner & Molly A. Maupin
The Point-Source Load Estimation Tool (PSLoadEsT) provides a user-friendly interface for generating reproducible load calculations for point source dischargers while managing common data challenges including duplicates, incompatible input tables, and incomplete or missing nutrient concentration or effluent flow data. Maintaining a consistent method across an entire study area is important when estimating loads to be used as calibration data for regional water-quality models. PSLoadEsT is written using the open-source programming language R and has an...

Floodplain and Channel Evaluation Tool: FACET

Samuel Lamont, Labeeb Ahmed, Marina Metes, Kristina Hopkins, Peter Claggett & Gregory Noe
FACET is a Python tool that uses open source modules to map the floodplain extent and derive reach-scale summaries of stream and floodplain geomorphic measurements from high-resolution digital elevation models (DEMs). Geomorphic measurements include channel width, stream bank height, floodplain width, and stream slope. FACET allows the user to hydrologically condition the DEM, generate the stream network, select one of two options for stream bank identification, map the floodplain extent using a Height Above Nearest...

bbsAssistant: An R package for downloading and handling data and information from the North American Breeding Bird Survey.

Jessica Burnett, Lyndsie S Wszola & Gabriela Palomo-Munoz
This R package contains functions for downloading and munging data from the North American Breeding Bird Survey (BBS) via FTP (Pardieck et al. 2018; J. R. Sauer et al. 2017). This package was created to allow the user to bulk-download the BBS point count and related (e.g., route-level conditions) via FTP, and to quickly subset the data by taxonomic classifications and/or geographical locations. This package also maintains data containing the trend and annual indices from...

MODFLOW-2005: USGS three-dimensional finite-difference groundwater model

Arlen W. Harbaugh, Christian D. Langevin, Joseph D. Hughes, Richard G. Niswonger & Leonard F Konikow
MODFLOW is a three-dimensional (3D) finite-difference groundwater model that was first published in 1984. It has a modular structure that allows it to be easily modified to adapt the code for a particular application. Many new capabilities have been added to the original model. MODFLOW 6 is presently the core MODFLOW version distributed by the USGS, but MODFLOW-2005 (the previous core version) is still actively maintained and supported. MODFLOW-2005 (Harbaugh, 2005) simulates steady and nonsteady...

FluEgg

Marian M Domanski

CWDsims: An R package to run chronic wasting disease (CWD) models and a Shiny app

Paul C Cross & Emily S. Almberg

Electromagnetic Transfer Function File Conversion Utilities (EMTF FCU)

Anna Kelbert
Magnetotelluric impedances and other similar transfer functions are important for geophysical interpretation and for space weather hazards. I helped develop and continue to curate a database known as IRIS EMTF, http://ds.iris.edu/spud/emtf which uses something called EMTF XML format for storing the data. EMTF FCU v4.1 software consists of a set of freely available format conversion tools that can be used to convert these files to and from historical formats, rotate the data to alternative coordinate...

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